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b/cgi-bin/data/bamdata_Developmental_transcriptome.xml index 781f077..ac28d4e 100644 --- a/cgi-bin/data/bamdata_Developmental_transcriptome.xml +++ b/cgi-bin/data/bamdata_Developmental_transcriptome.xml @@ -1,7 +1,7 @@ - + @@ -10,7 +10,7 @@ - + @@ -19,7 +19,7 @@ - + @@ -28,7 +28,7 @@ - + @@ -37,7 +37,7 @@ - + @@ -46,7 +46,7 @@ - + @@ -55,7 +55,7 @@ - + @@ -64,7 +64,7 @@ - + @@ -73,7 +73,7 @@ - + @@ -82,7 +82,7 @@ - + @@ -91,7 +91,7 @@ - + @@ -100,7 +100,7 @@ - + @@ -109,7 +109,7 @@ - + @@ -118,7 +118,7 @@ - + @@ -127,7 +127,7 @@ - + @@ -136,7 +136,7 @@ - + @@ -145,7 +145,7 @@ - + @@ -154,7 +154,7 @@ - + @@ -163,7 +163,7 @@ - + @@ -172,7 +172,7 @@ - + @@ -181,7 +181,7 @@ - + @@ -190,7 +190,7 @@ - + @@ -199,7 +199,7 @@ - + @@ -208,7 +208,7 @@ - + @@ -217,7 +217,7 @@ - + @@ -226,7 +226,7 @@ - + @@ -235,7 +235,7 @@ - + @@ -244,7 +244,7 @@ - + @@ -253,7 +253,7 @@ - + @@ -262,7 +262,7 @@ - + @@ -271,7 +271,7 @@ - + @@ -280,7 +280,7 @@ - + @@ -289,7 +289,7 @@ - + @@ -298,7 +298,7 @@ - + @@ -307,7 +307,7 @@ - + @@ -316,7 +316,7 @@ - + @@ -325,7 +325,7 @@ - + @@ -334,7 +334,7 @@ - + @@ -343,7 +343,7 @@ - + @@ -352,7 +352,7 @@ - + @@ -361,7 +361,7 @@ - + @@ -370,7 +370,7 @@ - + @@ -379,7 +379,7 @@ - + @@ -388,7 +388,7 @@ - + @@ -397,7 +397,7 @@ - + @@ -406,7 +406,7 @@ - + @@ -415,7 +415,7 @@ - + @@ -424,7 +424,7 @@ - + @@ -433,7 +433,7 @@ - + @@ -442,7 +442,7 @@ - + @@ -451,7 +451,7 @@ - + @@ -460,7 +460,7 @@ - + @@ -469,7 +469,7 @@ - + @@ -478,7 +478,7 @@ - + @@ -487,7 +487,7 @@ - + @@ -496,7 +496,7 @@ - + @@ -505,7 +505,7 @@ - + @@ -514,7 +514,7 @@ - + @@ -523,7 +523,7 @@ - + @@ -532,7 +532,7 @@ - + @@ -541,7 +541,7 @@ - + @@ -550,7 +550,7 @@ - + @@ -559,7 +559,7 @@ - + @@ -568,7 +568,7 @@ - + @@ -577,7 +577,7 @@ - + @@ -586,7 +586,7 @@ - + @@ -595,7 +595,7 @@ - + @@ -604,7 +604,7 @@ - + @@ -613,7 +613,7 @@ - + @@ -622,7 +622,7 @@ - + @@ -631,7 +631,7 @@ - + @@ -640,7 +640,7 @@ - + @@ -649,7 +649,7 @@ - + @@ -658,7 +658,7 @@ - + @@ -667,7 +667,7 @@ - + @@ -676,7 +676,7 @@ - + @@ -685,7 +685,7 @@ - + @@ -694,7 +694,7 @@ - + @@ -703,7 +703,7 @@ - + @@ -712,7 +712,7 @@ - + @@ -721,7 +721,7 @@ - + @@ -730,7 +730,7 @@ - + @@ -739,7 +739,7 @@ - + @@ -748,7 +748,7 @@ - + @@ -757,7 +757,7 @@ - + @@ -766,7 +766,7 @@ - + @@ -775,7 +775,7 @@ - + @@ -784,7 +784,7 @@ - + @@ -793,7 +793,7 @@ - + @@ -802,7 +802,7 @@ - + @@ -811,7 +811,7 @@ - + @@ -820,7 +820,7 @@ - + @@ -829,7 +829,7 @@ - + @@ -838,7 +838,7 @@ - + @@ -847,7 +847,7 @@ - + @@ -856,7 +856,7 @@ - + @@ -865,7 +865,7 @@ - + @@ -874,7 +874,7 @@ - + @@ -883,7 +883,7 @@ - + @@ -892,7 +892,7 @@ - + @@ -901,7 +901,7 @@ - + @@ -910,7 +910,7 @@ - + @@ -919,7 +919,7 @@ - + @@ -928,7 +928,7 @@ - + @@ -937,7 +937,7 @@ - + @@ -946,7 +946,7 @@ - + @@ -955,7 +955,7 @@ - + @@ -964,7 +964,7 @@ - + @@ -973,7 +973,7 @@ - + @@ -982,7 +982,7 @@ - + @@ -991,7 +991,7 @@ - + @@ -1000,7 +1000,7 @@ - + @@ -1009,7 +1009,7 @@ - + @@ -1018,7 +1018,7 @@ - + @@ -1027,7 +1027,7 @@ - + @@ -1036,7 +1036,7 @@ - + @@ -1045,7 +1045,7 @@ - + @@ -1054,7 +1054,7 @@ - + @@ -1063,7 +1063,7 @@ - + @@ -1072,7 +1072,7 @@ - + @@ -1081,7 +1081,7 @@ - + @@ -1090,7 +1090,7 @@ - + @@ -1099,7 +1099,7 @@ - + @@ -1108,7 +1108,7 @@ - + @@ -1117,7 +1117,7 @@ - + @@ -1126,7 +1126,7 @@ - + @@ -1135,7 +1135,7 @@ - + @@ -1144,7 +1144,7 @@ - + @@ -1153,7 +1153,7 @@ - + @@ -1162,7 +1162,7 @@ - + @@ -1171,7 +1171,7 @@ - + @@ -1180,7 +1180,7 @@ - + @@ -1189,7 +1189,7 @@ - + @@ -1198,7 +1198,7 @@ - + @@ -1207,7 +1207,7 @@ - + @@ -1216,7 +1216,7 @@ - + @@ -1225,7 +1225,7 @@ - + @@ -1234,7 +1234,7 @@ - + @@ -1243,7 +1243,7 @@ - + @@ -1252,7 +1252,7 @@ - + @@ -1261,7 +1261,7 @@ - + @@ -1270,7 +1270,7 @@ - + @@ -1279,7 +1279,7 @@ - + @@ -1288,7 +1288,7 @@ - + @@ -1297,7 +1297,7 @@ - + @@ -1307,7 +1307,7 @@ - + @@ -1326,7 +1326,7 @@ - + @@ -1335,7 +1335,7 @@ - + @@ -1344,7 +1344,7 @@ - + @@ -1353,7 +1353,7 @@ - + @@ -1362,7 +1362,7 @@ - + @@ -1371,7 +1371,7 @@ - + @@ -1380,7 +1380,7 @@ - + @@ -1389,7 +1389,7 @@ - + @@ -1398,7 +1398,7 @@ - + @@ -1407,7 +1407,7 @@ - + @@ -1416,7 +1416,7 @@ - + @@ -1425,7 +1425,7 @@ - + @@ -1434,7 +1434,7 @@ - + @@ -1443,7 +1443,7 @@ - + @@ -1452,7 +1452,7 @@ - + @@ -1461,7 +1461,7 @@ - + @@ -1470,7 +1470,7 @@ - + @@ -1479,7 +1479,7 @@ - + @@ -1488,7 +1488,7 @@ - + @@ -1497,7 +1497,7 @@ - + @@ -1506,7 +1506,7 @@ - + @@ -1516,7 +1516,7 @@ - + @@ -1535,7 +1535,7 @@ - + @@ -1544,7 +1544,7 @@ - + diff --git a/cgi-bin/data/bamdata_araport11.xml b/cgi-bin/data/bamdata_araport11.xml index 47cb389..af5bb43 100644 --- a/cgi-bin/data/bamdata_araport11.xml +++ b/cgi-bin/data/bamdata_araport11.xml @@ -1,6 +1,6 @@ - + ERR274310 @@ -11,7 +11,7 @@ ERR274311 - + SRR547531 @@ -21,7 +21,7 @@ SRR547533 - + SRR548277 @@ -30,7 +30,7 @@ SRR548278 - + SRR847501 SRR847502 @@ -44,7 +44,7 @@ SRR847506 - + SRR847501 SRR847502 @@ -58,7 +58,7 @@ SRR847506 - + SRR847501 SRR847502 @@ -72,7 +72,7 @@ SRR847506 - + SRR847501 SRR847502 @@ -86,7 +86,7 @@ SRR847506 - + SRR1207194 SRR1207195 @@ -102,7 +102,7 @@ SRR1207201 - + SRR1207194 SRR1207195 @@ -118,7 +118,7 @@ SRR1207201 - + SRR1019436 SRR1019437 @@ -136,7 +136,7 @@ SRR1019443 - + SRR1019436 SRR1019437 @@ -154,7 +154,7 @@ SRR1019443 - + SRR1049777 SRR1049778 @@ -185,7 +185,7 @@ SRR1049788 - + SRR477075 SRR477076 @@ -201,7 +201,7 @@ SRR477082 - + SRR477075 SRR477076 @@ -217,7 +217,7 @@ SRR477082 - + SRR493237 SRR493238 @@ -235,7 +235,7 @@ SRR493290 - + SRR493237 SRR493238 @@ -253,7 +253,7 @@ SRR493290 - + MEDIAN @@ -266,7 +266,7 @@ SRR314818 - + SRR800753 SRR800754 @@ -276,7 +276,7 @@ SRR800754 - + SRR800753 SRR800754 @@ -286,7 +286,7 @@ SRR800754 - + SRR1105822 SRR1105823 @@ -307,7 +307,7 @@ SRR1106559 - + SRR1105822 SRR1105823 @@ -328,7 +328,7 @@ SRR1106559 - + SRR1159821 SRR1159827 @@ -363,7 +363,7 @@ SRR1264996 - + SRR1159821 SRR1159827 @@ -398,7 +398,7 @@ SRR1264996 - + SRR1159821 SRR1159827 @@ -433,7 +433,7 @@ SRR1264996 - + MEDIAN @@ -446,7 +446,7 @@ SRR314818 - + SRR446027 SRR446028 @@ -476,7 +476,7 @@ SRR446044 - + SRR446027 SRR446028 @@ -506,7 +506,7 @@ SRR446044 - + SRR446027 SRR446028 @@ -536,7 +536,7 @@ SRR446044 - + SRR446027 SRR446028 @@ -566,7 +566,7 @@ SRR446044 - + SRR446027 SRR446028 @@ -596,7 +596,7 @@ SRR446044 - + SRR446027 SRR446028 @@ -626,7 +626,7 @@ SRR446044 - + SRR446484 SRR446486 @@ -638,7 +638,7 @@ SRR446487 - + SRR446484 SRR446486 @@ -650,7 +650,7 @@ SRR446487 - + SRR446484 SRR446486 @@ -662,7 +662,7 @@ SRR446487 - + SRR446484 SRR446486 @@ -674,7 +674,7 @@ SRR446487 - + SRR493033 SRR493036 @@ -711,7 +711,7 @@ SRR681004 - + SRR492930 SRR492931 @@ -780,7 +780,7 @@ SRR513743 - + SRR492930 SRR492931 @@ -849,7 +849,7 @@ SRR513743 - + SRR492930 SRR492931 @@ -917,7 +917,7 @@ SRR513743 - + SRR764885 @@ -927,7 +927,7 @@ SRR764887 - + SRR924656 SRR925853 @@ -951,7 +951,7 @@ SRR925864 - + SRR934391 @@ -960,7 +960,7 @@ SRR934392 - + SRR941999 SRR942000 @@ -1014,7 +1014,7 @@ SRR942037 - + SRR070570 SRR070571 @@ -1026,7 +1026,7 @@ SRR070573 - + SRR070570 SRR070571 @@ -1038,7 +1038,7 @@ SRR070573 - + SRR1001909 SRR1001910 @@ -1056,7 +1056,7 @@ SRR1001910 - + SRR1001909 SRR1001910 @@ -1074,7 +1074,7 @@ SRR1001910 - + SRR1019221 @@ -1083,7 +1083,7 @@ SRR1019222 - + SRR345561 SRR345562 @@ -1095,7 +1095,7 @@ SRR345564 - + SRR345561 SRR345562 @@ -1107,7 +1107,7 @@ SRR345564 - + SRR346552 SRR346553 @@ -1117,7 +1117,7 @@ SRR346553 - + SRR346552 SRR346553 @@ -1127,7 +1127,7 @@ SRR346553 - + SRR394082 @@ -1139,7 +1139,7 @@ SRR394082 - + SRR504179 SRR504180 @@ -1160,7 +1160,7 @@ SRR576329 - + SRR504179 SRR504180 @@ -1181,7 +1181,7 @@ SRR576329 - + SRR504179 SRR504180 @@ -1202,7 +1202,7 @@ SRR576329 - + SRR515071 SRR515072 @@ -1215,7 +1215,7 @@ SRR515074 - + SRR515071 SRR515072 @@ -1228,7 +1228,7 @@ SRR515074 - + SRR527164 SRR527165 @@ -1243,7 +1243,7 @@ SRR527175 - + SRR527164 SRR527165 @@ -1258,7 +1258,7 @@ SRR527175 - + SRR584115 SRR584119 @@ -1282,7 +1282,7 @@ SRR584126 - + SRR584115 SRR584119 @@ -1306,7 +1306,7 @@ SRR584126 - + SRR584129 SRR584134 @@ -1325,7 +1325,7 @@ SRR584137 - + SRR584129 SRR584134 @@ -1344,7 +1344,7 @@ SRR584137 - + SRR653555 SRR653556 @@ -1413,7 +1413,7 @@ SRR653596 - + SRR653555 SRR653556 @@ -1482,7 +1482,7 @@ SRR653596 - + SRR653555 SRR653556 @@ -1551,7 +1551,7 @@ SRR653596 - + SRR653555 SRR653556 @@ -1620,7 +1620,7 @@ SRR653596 - + SRR653555 SRR653556 @@ -1689,7 +1689,7 @@ SRR653596 - + SRR653555 SRR653556 @@ -1758,7 +1758,7 @@ SRR653596 - + SRR653555 SRR653556 @@ -1827,7 +1827,7 @@ SRR653596 - + SRR653555 SRR653556 @@ -1896,7 +1896,7 @@ SRR653596 - + SRR653555 SRR653556 @@ -1965,7 +1965,7 @@ SRR653596 - + SRR653555 SRR653556 @@ -2034,7 +2034,7 @@ SRR653596 - + SRR653555 SRR653556 @@ -2103,7 +2103,7 @@ SRR653596 - + SRR653555 SRR653556 @@ -2172,7 +2172,7 @@ SRR653596 - + SRR653555 SRR653556 @@ -2241,7 +2241,7 @@ SRR653596 - + SRR653555 SRR653556 @@ -2310,7 +2310,7 @@ SRR653596 - + SRR653555 SRR653556 @@ -2379,7 +2379,7 @@ SRR653596 - + SRR653555 SRR653556 @@ -2448,7 +2448,7 @@ SRR653596 - + SRR653555 SRR653556 @@ -2517,7 +2517,7 @@ SRR653596 - + SRR653555 SRR653556 @@ -2586,7 +2586,7 @@ SRR653596 - + SRR653555 SRR653556 @@ -2655,7 +2655,7 @@ SRR653596 - + SRR653555 SRR653556 @@ -2724,7 +2724,7 @@ SRR653596 - + SRR653555 SRR653556 @@ -2793,7 +2793,7 @@ SRR653596 - + SRR797194 SRR797230 @@ -2808,7 +2808,7 @@ SRR833246 - + SRR797194 SRR797230 @@ -2823,7 +2823,7 @@ SRR833246 - + SRR797194 SRR797230 @@ -2838,7 +2838,7 @@ SRR833246 - + SRR847503 SRR847504 @@ -2854,7 +2854,7 @@ SRR847506 - + SRR847503 SRR847504 @@ -2870,7 +2870,7 @@ SRR847506 - + SRR1260032 SRR1260033 @@ -2888,7 +2888,7 @@ SRR1286088 - + SRR1260032 SRR1260033 @@ -2906,7 +2906,7 @@ SRR1286088 - + SRR1261509 @@ -2915,7 +2915,7 @@ SRR1261509 - + SRR401413 SRR401414 @@ -2948,7 +2948,7 @@ SRR401430 - + SRR401413 SRR401414 @@ -2981,7 +2981,7 @@ SRR401430 - + SRR401413 SRR401414 @@ -3014,7 +3014,7 @@ SRR401430 - + SRR401413 SRR401414 @@ -3047,7 +3047,7 @@ SRR401430 - + SRR401413 SRR401414 @@ -3080,7 +3080,7 @@ SRR401430 - + SRR401413 SRR401414 @@ -3113,7 +3113,7 @@ SRR401430 - + SRR401413 SRR401414 @@ -3146,7 +3146,7 @@ SRR401430 - + SRR401413 SRR401414 @@ -3179,7 +3179,7 @@ SRR401430 - + SRR401413 SRR401414 @@ -3212,7 +3212,7 @@ SRR401430 - + ERR274310 @@ -3223,7 +3223,7 @@ ERR274311 - + SRR1046909 SRR1046910 @@ -3269,7 +3269,7 @@ SRR1046942 - + SRR1046909 SRR1046910 @@ -3315,7 +3315,7 @@ SRR1046942 - + SRR1524941 SRR1524945 @@ -3330,7 +3330,7 @@ SRR1524946 - + SRR1524941 SRR1524945 @@ -3345,7 +3345,7 @@ SRR1524946 - + SRR1524941 SRR1524945 @@ -3360,7 +3360,7 @@ SRR1524946 - + MEDIAN @@ -3373,7 +3373,7 @@ SRR314818 - + SRR949956 SRR949965 @@ -3391,7 +3391,7 @@ SRR949993 - + SRR949956 SRR949965 @@ -3409,7 +3409,7 @@ SRR949993 - + SRR949956 SRR949965 @@ -3427,7 +3427,7 @@ SRR949993 - + SRR949956 SRR949965 diff --git a/cgi-bin/data/carpel/SRR1207194/accepted_hits.bam.bai b/cgi-bin/data/carpel/SRR1207194/accepted_hits.bam.bai deleted file mode 100644 index e43ea64..0000000 Binary files a/cgi-bin/data/carpel/SRR1207194/accepted_hits.bam.bai and /dev/null differ diff --git a/cgi-bin/data/carpel/SRR1207195/accepted_hits.bam.bai b/cgi-bin/data/carpel/SRR1207195/accepted_hits.bam.bai deleted file mode 100644 index 1665a1f..0000000 Binary files a/cgi-bin/data/carpel/SRR1207195/accepted_hits.bam.bai and /dev/null differ diff --git a/cgi-bin/data/dark/SRR1019436/accepted_hits.bam.bai b/cgi-bin/data/dark/SRR1019436/accepted_hits.bam.bai deleted file mode 100644 index 62a2417..0000000 Binary files a/cgi-bin/data/dark/SRR1019436/accepted_hits.bam.bai and /dev/null differ diff --git a/cgi-bin/data/dark/SRR1019437/accepted_hits.bam.bai b/cgi-bin/data/dark/SRR1019437/accepted_hits.bam.bai deleted file mode 100644 index 29e6b7d..0000000 Binary files a/cgi-bin/data/dark/SRR1019437/accepted_hits.bam.bai and /dev/null differ diff --git a/cgi-bin/data/dark/SRR1049784/accepted_hits.bam.bai b/cgi-bin/data/dark/SRR1049784/accepted_hits.bam.bai deleted file mode 100644 index a1caef0..0000000 Binary files a/cgi-bin/data/dark/SRR1049784/accepted_hits.bam.bai and /dev/null differ diff --git a/cgi-bin/data/dark/SRR477075/accepted_hits.bam.bai b/cgi-bin/data/dark/SRR477075/accepted_hits.bam.bai deleted file mode 100644 index eb3bc9f..0000000 Binary files a/cgi-bin/data/dark/SRR477075/accepted_hits.bam.bai and /dev/null differ diff --git a/cgi-bin/data/dark/SRR477076/accepted_hits.bam.bai b/cgi-bin/data/dark/SRR477076/accepted_hits.bam.bai deleted file mode 100644 index 479bcbb..0000000 Binary files a/cgi-bin/data/dark/SRR477076/accepted_hits.bam.bai and /dev/null differ diff --git a/cgi-bin/data/dark/SRR493237/accepted_hits.bam.bai b/cgi-bin/data/dark/SRR493237/accepted_hits.bam.bai deleted file mode 100644 index 3e8618e..0000000 Binary files a/cgi-bin/data/dark/SRR493237/accepted_hits.bam.bai and /dev/null differ diff --git a/cgi-bin/data/dark/SRR493238/accepted_hits.bam.bai b/cgi-bin/data/dark/SRR493238/accepted_hits.bam.bai deleted file mode 100644 index e689165..0000000 Binary files a/cgi-bin/data/dark/SRR493238/accepted_hits.bam.bai and /dev/null differ diff --git a/cgi-bin/data/flower/SRR314815/accepted_hits.bam.bai b/cgi-bin/data/flower/SRR314815/accepted_hits.bam.bai deleted file mode 100644 index 59bad33..0000000 Binary files a/cgi-bin/data/flower/SRR314815/accepted_hits.bam.bai and /dev/null differ diff --git a/cgi-bin/data/flower/SRR800753/accepted_hits.bam.bai b/cgi-bin/data/flower/SRR800753/accepted_hits.bam.bai deleted file mode 100644 index 8d7ad47..0000000 Binary files a/cgi-bin/data/flower/SRR800753/accepted_hits.bam.bai and /dev/null differ diff --git a/cgi-bin/data/flower/SRR800754/accepted_hits.bam.bai b/cgi-bin/data/flower/SRR800754/accepted_hits.bam.bai deleted file mode 100644 index 8a3fc7b..0000000 Binary files a/cgi-bin/data/flower/SRR800754/accepted_hits.bam.bai and /dev/null differ diff --git a/cgi-bin/data/guard_cell_drought.xml b/cgi-bin/data/guard_cell_drought.xml index bfb858a..77c8090 100644 --- a/cgi-bin/data/guard_cell_drought.xml +++ b/cgi-bin/data/guard_cell_drought.xml @@ -1,6 +1,6 @@ - + @@ -11,7 +11,7 @@ - + GC20w1 GC20w2 @@ -25,7 +25,7 @@ - + GC20w1 GC20w2 @@ -39,7 +39,7 @@ - + GC20d1 GC20d2 @@ -53,7 +53,7 @@ - + GC20d1 GC20d2 @@ -67,7 +67,7 @@ - + @@ -78,7 +78,7 @@ - + @@ -89,7 +89,7 @@ - + @@ -100,7 +100,7 @@ - + L20w1 L20w2 @@ -113,7 +113,7 @@ - + L20w1 L20w2 @@ -126,7 +126,7 @@ - + L20w1 L20w2 @@ -139,7 +139,7 @@ - + @@ -150,7 +150,7 @@ - + @@ -161,7 +161,7 @@ - + @@ -172,7 +172,7 @@ - + L40w1 L40w2 @@ -185,7 +185,7 @@ - + L40w1 L40w2 @@ -198,7 +198,7 @@ - + L40w1 L40w2 @@ -211,7 +211,7 @@ - + @@ -222,7 +222,7 @@ - + @@ -233,7 +233,7 @@ - + @@ -244,7 +244,7 @@ - + L60w1 L60w2 @@ -257,7 +257,7 @@ - + L60w1 L60w2 @@ -270,7 +270,7 @@ - + L60w1 L60w2 @@ -283,7 +283,7 @@ - + L20d1 L20d2 @@ -296,7 +296,7 @@ - + L20d1 L20d2 @@ -309,7 +309,7 @@ - + L20d1 L20d2 @@ -322,7 +322,7 @@ - + @@ -333,7 +333,7 @@ - + @@ -344,7 +344,7 @@ - + GC20w1 GC20w2 @@ -358,7 +358,7 @@ - + GC20w1 GC20w2 @@ -372,7 +372,7 @@ - + @@ -383,7 +383,7 @@ - + @@ -394,7 +394,7 @@ - + @@ -405,7 +405,7 @@ - + GC40w1 GC40w2 @@ -417,7 +417,7 @@ - + GC40w1 GC40w2 @@ -429,7 +429,7 @@ - + @@ -440,7 +440,7 @@ - + @@ -451,7 +451,7 @@ - + @@ -462,7 +462,7 @@ - + GC60w1 GC60w2 @@ -475,7 +475,7 @@ - + GC60w1 GC60w2 @@ -488,7 +488,7 @@ - + GC60w1 GC60w2 @@ -501,7 +501,7 @@ - + GC20d1 GC20d2 diff --git a/cgi-bin/data/leaf/SRR1105822/accepted_hits.bam.bai b/cgi-bin/data/leaf/SRR1105822/accepted_hits.bam.bai deleted file mode 100644 index 0396d47..0000000 Binary files a/cgi-bin/data/leaf/SRR1105822/accepted_hits.bam.bai and /dev/null differ diff --git a/cgi-bin/data/leaf/SRR1105823/accepted_hits.bam.bai b/cgi-bin/data/leaf/SRR1105823/accepted_hits.bam.bai deleted file mode 100644 index 7e8c54c..0000000 Binary files a/cgi-bin/data/leaf/SRR1105823/accepted_hits.bam.bai and /dev/null differ diff --git a/cgi-bin/data/leaf/SRR1159821/accepted_hits.bam.bai b/cgi-bin/data/leaf/SRR1159821/accepted_hits.bam.bai deleted file mode 100644 index 50fff5c..0000000 Binary files a/cgi-bin/data/leaf/SRR1159821/accepted_hits.bam.bai and /dev/null differ diff --git a/cgi-bin/data/leaf/SRR1159827/accepted_hits.bam.bai b/cgi-bin/data/leaf/SRR1159827/accepted_hits.bam.bai deleted file mode 100644 index e31abaa..0000000 Binary files a/cgi-bin/data/leaf/SRR1159827/accepted_hits.bam.bai and /dev/null differ diff --git a/cgi-bin/data/leaf/SRR1159837/accepted_hits.bam.bai b/cgi-bin/data/leaf/SRR1159837/accepted_hits.bam.bai deleted file mode 100644 index e6703d9..0000000 Binary files a/cgi-bin/data/leaf/SRR1159837/accepted_hits.bam.bai and /dev/null differ diff --git a/cgi-bin/data/leaf/SRR314813/accepted_hits.bam.bai b/cgi-bin/data/leaf/SRR314813/accepted_hits.bam.bai deleted file mode 100644 index 6f8bd5b..0000000 Binary files a/cgi-bin/data/leaf/SRR314813/accepted_hits.bam.bai and /dev/null differ diff --git a/cgi-bin/data/leaf/SRR446027/accepted_hits.bam.bai b/cgi-bin/data/leaf/SRR446027/accepted_hits.bam.bai deleted file mode 100644 index 8902d78..0000000 Binary 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+ @@ -11,7 +11,7 @@ - + @@ -22,7 +22,7 @@ - + @@ -33,7 +33,7 @@ - + @@ -44,7 +44,7 @@ - + @@ -55,7 +55,7 @@ - + @@ -66,7 +66,7 @@ - + @@ -77,7 +77,7 @@ - + @@ -88,7 +88,7 @@ - + @@ -99,7 +99,7 @@ - + @@ -110,7 +110,7 @@ - + @@ -121,7 +121,7 @@ - + @@ -132,7 +132,7 @@ - + @@ -143,7 +143,7 @@ - + @@ -154,7 +154,7 @@ - + @@ -165,7 +165,7 @@ - + @@ -176,7 +176,7 @@ - + @@ -187,7 +187,7 @@ - + @@ -198,7 +198,7 @@ - + @@ -209,7 +209,7 @@ - + @@ -220,7 +220,7 @@ - + @@ -231,7 +231,7 @@ - + @@ -242,7 +242,7 @@ - + @@ -253,7 +253,7 @@ - + @@ -264,7 +264,7 @@ - + @@ -275,7 +275,7 @@ - + @@ -286,7 +286,7 @@ - + @@ -297,7 +297,7 @@ - + @@ -308,7 +308,7 @@ - + @@ -319,7 +319,7 @@ - + diff --git a/cgi-bin/data/pollen/SRR847501/accepted_hits.bam.bai b/cgi-bin/data/pollen/SRR847501/accepted_hits.bam.bai deleted file mode 100644 index 2544d0f..0000000 Binary files a/cgi-bin/data/pollen/SRR847501/accepted_hits.bam.bai and /dev/null differ diff --git a/cgi-bin/data/pollen/SRR847502/accepted_hits.bam.bai b/cgi-bin/data/pollen/SRR847502/accepted_hits.bam.bai deleted file mode 100644 index 01de7cd..0000000 Binary files a/cgi-bin/data/pollen/SRR847502/accepted_hits.bam.bai and /dev/null differ diff --git a/cgi-bin/data/receptacle/SRR401413/accepted_hits.bam.bai b/cgi-bin/data/receptacle/SRR401413/accepted_hits.bam.bai deleted file mode 100644 index 10ab14a..0000000 Binary files a/cgi-bin/data/receptacle/SRR401413/accepted_hits.bam.bai and /dev/null differ diff --git a/cgi-bin/data/receptacle/SRR401414/accepted_hits.bam.bai b/cgi-bin/data/receptacle/SRR401414/accepted_hits.bam.bai deleted file mode 100644 index b0c3b99..0000000 Binary files a/cgi-bin/data/receptacle/SRR401414/accepted_hits.bam.bai and /dev/null differ diff --git a/cgi-bin/data/receptacle/SRR401415/accepted_hits.bam.bai b/cgi-bin/data/receptacle/SRR401415/accepted_hits.bam.bai deleted file mode 100644 index 65183ba..0000000 Binary files a/cgi-bin/data/receptacle/SRR401415/accepted_hits.bam.bai and /dev/null differ diff --git a/cgi-bin/data/receptacle/SRR401416/accepted_hits.bam.bai b/cgi-bin/data/receptacle/SRR401416/accepted_hits.bam.bai deleted file mode 100644 index efd3469..0000000 Binary files a/cgi-bin/data/receptacle/SRR401416/accepted_hits.bam.bai and /dev/null differ diff --git a/cgi-bin/data/receptacle/SRR401417/accepted_hits.bam.bai b/cgi-bin/data/receptacle/SRR401417/accepted_hits.bam.bai deleted file mode 100644 index 16b8bc8..0000000 Binary files a/cgi-bin/data/receptacle/SRR401417/accepted_hits.bam.bai and /dev/null differ diff --git a/cgi-bin/data/receptacle/SRR401418/accepted_hits.bam.bai b/cgi-bin/data/receptacle/SRR401418/accepted_hits.bam.bai deleted file mode 100644 index 85151f4..0000000 Binary files a/cgi-bin/data/receptacle/SRR401418/accepted_hits.bam.bai and /dev/null differ diff --git a/cgi-bin/data/receptacle/SRR401419/accepted_hits.bam.bai b/cgi-bin/data/receptacle/SRR401419/accepted_hits.bam.bai deleted file mode 100644 index 2e02063..0000000 Binary files a/cgi-bin/data/receptacle/SRR401419/accepted_hits.bam.bai and /dev/null differ diff --git a/cgi-bin/data/receptacle/SRR401420/accepted_hits.bam.bai b/cgi-bin/data/receptacle/SRR401420/accepted_hits.bam.bai deleted file mode 100644 index 9a0ee1b..0000000 Binary files a/cgi-bin/data/receptacle/SRR401420/accepted_hits.bam.bai and /dev/null differ diff --git a/cgi-bin/data/receptacle/SRR401421/accepted_hits.bam.bai b/cgi-bin/data/receptacle/SRR401421/accepted_hits.bam.bai deleted file mode 100644 index 0f2cb3d..0000000 Binary files a/cgi-bin/data/receptacle/SRR401421/accepted_hits.bam.bai and /dev/null differ diff --git a/cgi-bin/data/root/ERR274309/accepted_hits.bam.bai b/cgi-bin/data/root/ERR274309/accepted_hits.bam.bai deleted file mode 100644 index 1d30699..0000000 Binary files a/cgi-bin/data/root/ERR274309/accepted_hits.bam.bai and /dev/null differ diff --git a/cgi-bin/data/root/SRR1046909/accepted_hits.bam.bai b/cgi-bin/data/root/SRR1046909/accepted_hits.bam.bai deleted file mode 100644 index 4ede21b..0000000 Binary files a/cgi-bin/data/root/SRR1046909/accepted_hits.bam.bai and /dev/null differ diff --git a/cgi-bin/data/root/SRR1046910/accepted_hits.bam.bai b/cgi-bin/data/root/SRR1046910/accepted_hits.bam.bai deleted file mode 100644 index 27a2ec3..0000000 Binary files a/cgi-bin/data/root/SRR1046910/accepted_hits.bam.bai and /dev/null differ diff --git a/cgi-bin/data/root/SRR1524935/accepted_hits.bam.bai b/cgi-bin/data/root/SRR1524935/accepted_hits.bam.bai deleted file mode 100644 index df398f4..0000000 Binary files a/cgi-bin/data/root/SRR1524935/accepted_hits.bam.bai and /dev/null differ diff --git a/cgi-bin/data/root/SRR1524938/accepted_hits.bam.bai b/cgi-bin/data/root/SRR1524938/accepted_hits.bam.bai deleted file mode 100644 index 7da74db..0000000 Binary files a/cgi-bin/data/root/SRR1524938/accepted_hits.bam.bai and /dev/null differ diff --git a/cgi-bin/data/root/SRR1524940/accepted_hits.bam.bai b/cgi-bin/data/root/SRR1524940/accepted_hits.bam.bai deleted file mode 100644 index 610f97d..0000000 Binary files a/cgi-bin/data/root/SRR1524940/accepted_hits.bam.bai and /dev/null differ diff --git a/cgi-bin/data/root/SRR314814/accepted_hits.bam.bai b/cgi-bin/data/root/SRR314814/accepted_hits.bam.bai deleted file mode 100644 index 5f52047..0000000 Binary files a/cgi-bin/data/root/SRR314814/accepted_hits.bam.bai and /dev/null differ diff --git a/cgi-bin/rnaSeqMapCoverage.cgi b/cgi-bin/rnaSeqMapCoverage.cgi index 12f216e..682ad23 100755 --- a/cgi-bin/rnaSeqMapCoverage.cgi +++ b/cgi-bin/rnaSeqMapCoverage.cgi @@ -107,15 +107,8 @@ def determineReadMapNumber(filedir, filename, readMappedNumber, remoteDrive, bam readsMappedHold = [] # Holds the number # Clear temporary files and name a new one - os.system("find ../temp/* -mtime +1 -exec rm -f {} \\;") + os.system("find /var/www/html/eFP-Seq_Browser/temp/* -mtime +1 -exec rm -f {} \\;") - # Set the environment - bai_directory = ("data/" + filedir) - if os.path.isdir(bai_directory): - os.chdir(bai_directory) - else: - os.makedirs(bai_directory) - os.chdir(bai_directory) my_env = os.environ.copy() my_env["LD_LIBRARY_PATH"] = "/usr/local/lib/" @@ -126,8 +119,6 @@ def determineReadMapNumber(filedir, filename, readMappedNumber, remoteDrive, bam except: pass - os.chdir("../../../") - if flagstat is None: return "FAILED: determineReadMapNumber-flagstat NONE" @@ -152,21 +143,10 @@ def makeImage(filedir, filename, chromosome, start, end, record, yscale, hexcode x_bp_vals = [] # Holds nucleotide positions... y_reads_values = [] # Holds the valid mapped reads for the position... - if bamType == "Google Drive": - # Clear temporary files and name a new one - # os.system("find ../temp/* -mtime +1 -exec rm -f {} \\;") - tempfile = "../temp/RNASeqGraph.png" - # Call samtools and get mpileup region = chromosome + ":" + str(start) + "-" + str(end) # Set the environment - bai_directory = ("data/" + filedir) - if os.path.isdir(bai_directory): - os.chdir(bai_directory) - else: - os.makedirs(bai_directory) - os.chdir(bai_directory) my_env = os.environ.copy() my_env["LD_LIBRARY_PATH"] = "/usr/local/lib/" @@ -178,8 +158,6 @@ def makeImage(filedir, filename, chromosome, start, end, record, yscale, hexcode except: pass - os.chdir("../../../") - if mpileup is None: return "FAILED" @@ -247,9 +225,9 @@ def makeImage(filedir, filename, chromosome, start, end, record, yscale, hexcode if bamType == "Amazon AWS": # Clear temporary files and name a new one - os.system("find ../temp/* -mtime +1 -exec rm -f {} \\;") + os.system("find /var/www/html/eFP-Seq_Browser/temp/* -mtime +1 -exec rm -f {} \\;") - tempfile = "../temp/RNASeqGraph.png" + tempfile = "/var/www/html/eFP-Seq_Browser/temp/RNASeqGraph.png" # Output the GD image to temp PNG file f = open(tempfile, "wb") rnaseq_graph_image.save(f) @@ -263,7 +241,7 @@ def makeImage(filedir, filename, chromosome, start, end, record, yscale, hexcode ################################################################################ -# Ouput functions +# Output functions ################################################################################ # Error function def dumpError(result, locus=None, record=None, my_base64img=None, abs_fpkm=None, r=None, totalReadsMapped=None): @@ -401,63 +379,16 @@ def main(): expectedGeneLength.append(exonGeneLength) # Public datasets and their directories: + # There are no public record as of Sep 2025 publicDatapoints = { - 'aerial': ['ERR274310', 'SRR547531', 'SRR548277', 'SRR847503', 'SRR847504', 'SRR847505', 'SRR847506'], - 'carpel': ['SRR1207194', 'SRR1207195'], - 'dark': ['SRR1019436', 'SRR1019437', 'SRR1049784', 'SRR477075', 'SRR477076', 'SRR493237', 'SRR493238'], - 'flower': ['SRR314815', 'SRR800753', 'SRR800754'], - 'Klepikova': ['SRR3581336', 'SRR3581345', 'SRR3581346', 'SRR3581347', 'SRR3581352', 'SRR3581356', - 'SRR3581383', 'SRR3581388', 'SRR3581499', 'SRR3581591', 'SRR3581639', 'SRR3581672', - 'SRR3581676', 'SRR3581678', 'SRR3581679', 'SRR3581680', 'SRR3581681', 'SRR3581682', - 'SRR3581683', 'SRR3581684', 'SRR3581685', 'SRR3581686', 'SRR3581687', 'SRR3581688', - 'SRR3581689', 'SRR3581690', 'SRR3581691', 'SRR3581692', 'SRR3581693', 'SRR3581694', - 'SRR3581695', 'SRR3581696', 'SRR3581697', 'SRR3581698', 'SRR3581699', 'SRR3581700', - 'SRR3581701', 'SRR3581702', 'SRR3581703', 'SRR3581704', 'SRR3581705', 'SRR3581706', - 'SRR3581707', 'SRR3581708', 'SRR3581709', 'SRR3581710', 'SRR3581711', 'SRR3581712', - 'SRR3581713', 'SRR3581714', 'SRR3581715', 'SRR3581716', 'SRR3581717', 'SRR3581719', - 'SRR3581720', 'SRR3581721', 'SRR3581724', 'SRR3581726', 'SRR3581727', 'SRR3581728', - 'SRR3581730', 'SRR3581731', 'SRR3581732', 'SRR3581733', 'SRR3581734', 'SRR3581735', - 'SRR3581736', 'SRR3581737', 'SRR3581738', 'SRR3581740', 'SRR3581831', 'SRR3581833', - 'SRR3581834', 'SRR3581835', 'SRR3581836', 'SRR3581837', 'SRR3581838', 'SRR3581839', - 'SRR3581840', 'SRR3581841', 'SRR3581842', 'SRR3581843', 'SRR3581844', 'SRR3581845', - 'SRR3581846', 'SRR3581847', 'SRR3581848', 'SRR3581849', 'SRR3581850', 'SRR3581851', - 'SRR3581852', 'SRR3581853', 'SRR3581854', 'SRR3581855', 'SRR3581856', 'SRR3581857', - 'SRR3581858', 'SRR3581859', 'SRR3581860', 'SRR3581861', 'SRR3581862', 'SRR3581863', - 'SRR3581864', 'SRR3581865', 'SRR3581866', 'SRR3581867', 'SRR3581868', 'SRR3581869', - 'SRR3581870', 'SRR3581871', 'SRR3581872', 'SRR3581873', 'SRR3581874', 'SRR3581875', - 'SRR3581876', 'SRR3581877', 'SRR3581878', 'SRR3581879', 'SRR3581880', 'SRR3581881', - 'SRR3581882', 'SRR3581883', 'SRR3581884', 'SRR3581885', 'SRR3581886', 'SRR3581887', - 'SRR3581888', 'SRR3581889', 'SRR3581890', 'SRR3581891', 'SRR3581892', 'SRR3581893', - 'SRR3581894', 'SRR3581895', 'SRR3581896', 'SRR3581897', 'SRR3581898', 'SRR3581899', - 'SRR3724649', 'SRR3724650', 'SRR3724651', 'SRR3724652', 'SRR3724663', 'SRR3724668', - 'SRR3724737', 'SRR3724739', 'SRR3724741', 'SRR3724768', 'SRR3724774', 'SRR3724778', - 'SRR3724782', 'SRR3724785', 'SRR3724786', 'SRR3724787', 'SRR3724798', 'SRR3724806', - 'SRR3724814', 'SRR3725446', 'SRR3725458', 'SRR3725471', 'SRR3725482', 'SRR3725493', - 'SRR3725503', 'SRR3725516', 'SRR3725527', 'SRR3725538', 'SRR3725550', 'SRR3725561', - 'SRR847501', 'SRR847502'], - 'leaf': ['SRR1105822', 'SRR1105823', 'SRR1159821', 'SRR1159827', 'SRR1159837', 'SRR314813', 'SRR446027', - 'SRR446028', 'SRR446033', 'SRR446034', 'SRR446039', 'SRR446040', 'SRR446484', 'SRR446485', - 'SRR446486', 'SRR446487', 'SRR493036', 'SRR493097', 'SRR493098', 'SRR493101', 'SRR764885', - 'SRR924656', 'SRR934391', 'SRR942022'], - 'light': ['SRR070570', 'SRR070571', 'SRR1001909', 'SRR1001910', 'SRR1019221', 'SRR345561', 'SRR345562', - 'SRR346552', 'SRR346553', 'SRR394082', 'SRR504179', 'SRR504180', 'SRR504181', 'SRR515073', - 'SRR515074', 'SRR527164', 'SRR527165', 'SRR584115', 'SRR584121', 'SRR584129', 'SRR584134', - 'SRR653555', 'SRR653556', 'SRR653557', 'SRR653561', 'SRR653562', 'SRR653563', 'SRR653564', - 'SRR653565', 'SRR653566', 'SRR653567', 'SRR653568', 'SRR653569', 'SRR653570', 'SRR653571', - 'SRR653572', 'SRR653573', 'SRR653574', 'SRR653575', 'SRR653576', 'SRR653577', 'SRR653578', - 'SRR797194', 'SRR797230', 'SRR833246'], - 'pollen': ['SRR847501', 'SRR847502'], - 'RAM': ['SRR1260032', 'SRR1260033', 'SRR1261509'], - 'receptacle': ['SRR401413', 'SRR401414', 'SRR401415', 'SRR401416', 'SRR401417', 'SRR401418', 'SRR401419', - 'SRR401420', 'SRR401421'], - 'root': ['ERR274309', 'SRR1046909', 'SRR1046910', 'SRR1524935', 'SRR1524938', 'SRR1524940', 'SRR314814'], - 'SAM': ['SRR949956', 'SRR949965', 'SRR949988', 'SRR949989'] + } ### Generate BAM directory link bam_dir = '' # Reset bam_dir value # Check if data is public or private dataset if cachedDatapoints: + # This won't work after Sep 2025 for x in publicDatapoints: # If public, find tissue (x) to create bam_dir if record in publicDatapoints[x]: bam_dir = x + '/' + record @@ -472,80 +403,25 @@ def main(): else: bam_dir = "uploads" + "/unknownRecord_" + start_time + # Google Drive and Amazon AWS not longer works! bam_file = '' # Reset bam_file value - if bamType == "Google Drive": - # Create a Google Drive mount point and muont the bam file. - uniqId = str(random.randint(1, 1000000)) - try: - pid = subprocess.Popen(["perl", "gDriveMountFast.pl", remoteDrive, uniqId, bamfilename]) - except: - sys.exit(1) - - # Make S3FS filename here - bam_file = "/mnt/gDrive/" + remoteDrive + "_" + uniqId + "/" + bamfilename - - # Wait unilt the file is ready, without locking up the system forever, locking system for five minutes - startTime = time.time() - while not (os.path.isfile(bam_file)): - # pass - currentTime = time.time() - if currentTime > (startTime + 300): - subprocess.call(["fusermount", "-u", "/mnt/gDrive/" + remoteDrive + "_" + uniqId]) - subprocess.call(["rm", "-rf", "/mnt/gDrive/" + remoteDrive + "_" + uniqId]) - dumpError("Mounting timed out", locus, record, base64img, abs_fpkm, r, totalReadsMapped) - - # Now make a image using samtools - base64img = makeImage(bam_dir, bam_file, "Chr" + chromosome, start, end, record, yscale, hexcode, - remoteDrive, bamType) - - if base64img == "FAILED": - base64img = makeImage(bam_dir, bam_file, "chr" + chromosome, start, end, record, yscale, hexcode, - remoteDrive, bamType) - region = "chr" + str(chromosome) + ":" + str(start) + "-" + str(end) - - if base64img == "FAILED": - base64img = makeImage(bam_dir, bam_file, chromosome, start, end, record, yscale, hexcode, remoteDrive, - bamType) - - if base64img == "FAILED": - subprocess.call(["fusermount", "-u", "/mnt/gDrive/" + remoteDrive + "_" + uniqId]) - subprocess.call(["rm", "-rf", "/mnt/gDrive/" + remoteDrive + "_" + uniqId]) - dumpError("Failed to get data.", locus, record, base64img, abs_fpkm, r, totalReadsMapped) - - elif bamType == "Amazon AWS": - # Make S3FS filename here - bam_file = "s3://" + remoteDrive - # Now make a image using samtools - base64img = makeImage(bam_dir, bam_file, "Chr" + chromosome, start, end, record, yscale, hexcode, - remoteDrive, bamType) - if base64img == "FAILED": - base64img = makeImage(bam_dir, bam_file, "chr" + chromosome, start, end, record, yscale, hexcode, - remoteDrive, bamType) - region = "chr" + str(chromosome) + ":" + str(start) + "-" + str(end) + # Local + bam_file = remoteDrive - if base64img == "FAILED": - region = str(chromosome) + ":" + str(start) + "-" + str(end) - base64img = makeImage(bam_dir, bam_file, chromosome, start, end, record, yscale, hexcode, remoteDrive, - bamType) + # Now make an image using samtools + base64img = makeImage(bam_dir, bam_file, "Chr" + chromosome, start, end, record, yscale, hexcode, + remoteDrive, bamType) - else: - # Local - bam_file = remoteDrive - - # Now make an image using samtools - base64img = makeImage(bam_dir, bam_file, "Chr" + chromosome, start, end, record, yscale, hexcode, + if base64img == "FAILED": + base64img = makeImage(bam_dir, bam_file, "chr" + chromosome, start, end, record, yscale, hexcode, remoteDrive, bamType) + region = "chr" + str(chromosome) + ":" + str(start) + "-" + str(end) - if base64img == "FAILED": - base64img = makeImage(bam_dir, bam_file, "chr" + chromosome, start, end, record, yscale, hexcode, - remoteDrive, bamType) - region = "chr" + str(chromosome) + ":" + str(start) + "-" + str(end) - - if base64img == "FAILED": - region = str(chromosome) + ":" + str(start) + "-" + str(end) - base64img = makeImage(bam_dir, bam_file, chromosome, start, end, record, yscale, hexcode, remoteDrive, + if base64img == "FAILED": + region = str(chromosome) + ":" + str(start) + "-" + str(end) + base64img = makeImage(bam_dir, bam_file, chromosome, start, end, record, yscale, hexcode, remoteDrive, bamType) # Correct total reads mapped: @@ -607,12 +483,6 @@ def main(): # the same info would be there. So just pass that along instead of # making this call .. to speed things up # Set the environment - bai_directory = ("data/" + bam_dir) - if os.path.isdir(bai_directory): - os.chdir(bai_directory) - else: - os.makedirs(bai_directory) - os.chdir(bai_directory) my_env = os.environ my_env["LD_LIBRARY_PATH"] = "/usr/local/lib/" @@ -623,12 +493,11 @@ def main(): except: dumpError("Unable to retrieve BAM data", locus, record, base64img, abs_fpkm, r, totalReadsMapped) - os.chdir("../../../") # Change this if FPKM is wrong for local data - if bamType == "local": - mapped_reads = lines.lower().count("\t" + chromosome + "\t") - else: + # Sep 2025 + mapped_reads = lines.lower().count("\t" + chromosome + "\t") + if mapped_reads == 0: mapped_reads = lines.lower().count('chr') abs_fpkm = [] @@ -647,16 +516,6 @@ def main(): r_val = float(sp / (math.sqrt(ss_x[i] * ss_y))) r.append(round(r_val, PRECISION)) - if bamType == "Google Drive": - try: - subprocess.call(["fusermount", "-u", "/mnt/gDrive/" + remoteDrive + "_" + uniqId]) - except: - sys.stderr.write("Failed to unmount FUSE file system.") - - try: - subprocess.call(["rm", "-rf", "/mnt/gDrive/" + remoteDrive + "_" + uniqId]) - except: - sys.stderr.write("Failed to delete FUSE mount point.") RNASeq_ReadsPerNucleotide = base64img[1]