Rename the format and modify the output file name

jlhg · Jan 29, 2013 · 6ed47a1 · 6ed47a1
1 parent 0deb5bb
commit 6ed47a1
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Showing 7 changed files with 25 additions and 16 deletions.
diff --git a/bdorpy/blast2accmap.py b/bdorpy/blast2accmap.py
@@ -7,7 +7,7 @@
 # http://opensource.org/licenses/MIT
 #
 # Author: Jian-Long Huang (jianlong@ntu.edu.tw)
-# Version: 0.1
+# Version: 0.2
 # Created: 2013.1.25
 #
 # Required:
@@ -23,7 +23,7 @@
 #
 # File Formats:
 # * blast.xml: blast XML
-# * output: blast-accmap
+# * output: blastaccmap
 
 import sys
 import argparse
@@ -40,11 +40,14 @@ def main():
                         help='evalue thresh (default: 0.01)')
     parser.add_argument('-t', '--min_hit_num', dest='min_hit_num', type=int, default=1,
                         help='minimum number of hit sequences (default: 1)')
-    parser.add_argument('-o', '--output', dest='output_file', default='blast2accmap_output_' + name.genid() + '.tsv',
+    parser.add_argument('-o', '--output', dest='output_file',
                         help='output file name. If this option is not specified, the script will generate '
                         'one with unique identifier at current directory.')
     args = parser.parse_args()
 
+    if args.output_file is None:
+        args.output_file = args.input_file + '_out_' + name.genid() + 'blastaccmap'
+
     total_query_num = 0
     parsed_query_num = 0
 

diff --git a/bdorpy/blastparser.py b/bdorpy/blastparser.py
@@ -7,7 +7,7 @@
 # http://opensource.org/licenses/MIT
 #
 # Author: Jian-Long Huang (jianlong@ntu.edu.tw)
-# Version: 2.0
+# Version: 2.1
 # Created: 2013.1.22
 #
 # Required :
@@ -34,7 +34,7 @@
 #
 # File formats:
 # * blast.xml: NCBI blast XML
-# * output: blast-list
+# * output: blastlist
 #
 # Tested:
 # * BLASTN 2.2.27+
@@ -57,7 +57,7 @@ def main():
                         help='evalue thresh (default: 0.01)')
     parser.add_argument('-r', '--rank', dest='aln_rank', type=int, default=250,
                         help='alignment rank (default: 250)')
-    parser.add_argument('-o', '--output', dest='output_file', default='bp_output_' + name.genid() + '.tsv',
+    parser.add_argument('-o', '--output', dest='output_file',
                         help='output file name. If this option is not specified, the script will generate '
                         'one with unique identifier at current directory.')
     parser.add_argument('-b', '--best', dest='best_hit', action='store_true', default=False,
@@ -76,6 +76,9 @@ def main():
     if args.best_hit is True:
         args.aln_rank = 1
 
+    if args.output_file is None:
+        args.output_file = args.input_file + '_out_' + name.genid() + '.blastlist'
+
     with open(args.intput_file, 'r') as result_handle, open(args.output_file, 'w') as fw:
         for i in proglog.start_message():
             fw.write(i)

diff --git a/bdorpy/cquery.py b/bdorpy/cquery.py
@@ -7,16 +7,16 @@
 # http://opensource.org/licenses/MIT
 #
 # Author: Jian-Long Huang (jianlong@ntu.edu.tw)
-# Version: 1.0
+# Version: 1.1
 # Created: 2013.1.23
 #
-# Usage: cquery <input.tsv>
+# Usage: cquery <input.blastlist>
 #
 # Options:
 # -e, --evalue NUM: evalue thresh (default: 0.01)
 #
 # File formats:
-# * input.tsv: blast-list
+# * input.blastlist: blastlist
 #
 # Support multiple input files and Unix style pathname pattern.
 #

diff --git a/bdorpy/fa2lens.py b/bdorpy/fa2lens.py
@@ -7,7 +7,7 @@
 # http://opensource.org/licenses/MIT
 #
 # Author: Jian-Long Huang (jianlong@ntu.edu.tw)
-# Version: 0.1
+# Version: 0.2
 # Created: 2013.1.26
 #
 # Required:
@@ -33,11 +33,14 @@ def main():
     parser.add_argument('input_file')
     parser.add_argument('-s', '--sep', dest='sep', default='\n',
                         help='seperator (default: newline)')
-    parser.add_argument('-o', '--output', dest='output_file', default='fa2lens_output_' + name.genid() + '.txt',
+    parser.add_argument('-o', '--output', dest='output_file',
                         help='output file name. If this option is not specified, the script will generate '
                         'one with unique identifier at current directory.')
     args = parser.parse_args()
 
+    if args.output_file is None:
+        args.output_file = args.input_file + '_out_' + name.genid() + '.leng.txt'
+
     with open(args.input_file, 'r') as fin, open(args.output_file, 'w') as fw:
         records = map(str, map(len, list(SeqIO.parse(fin, 'fasta'))))
         fw.write(args.sep.join(records))

diff --git a/bdorpy/fetchfa.py b/bdorpy/fetchfa.py
@@ -7,13 +7,13 @@
 # http://opensource.org/licenses/MIT
 #
 # Author: Jian-Long Huang (jianlong@ntu.edu.tw)
-# Version: 0.2
+# Version: 0.3
 # Created: 2013.1.24
 #
 # Required:
 # * Biopython: http://biopython.org
 #
-# Usage: batchgfa <input.tsv> [options]
+# Usage: batchgfa <input.blastaccmap> [options]
 # -d, --db     STR: database (default: protein)
 # -q, --query  STR: accessions to be fetched. If this option is specifid, the script will use the values
 #                   to fetch data, and no input file is required to be handled.
@@ -23,7 +23,7 @@
 # -l, --log    STR: log file name
 #
 # File formats:
-# * input.tsv: blast-accmap
+# * input.blastaccmap: blastaccmap
 # * output: fasta
 
 import os

diff --git a/docs/format/blast-accmap.txt → docs/format/blastaccmap.txt b/docs/format/blast-accmap.txt → docs/format/blastaccmap.txt
@@ -1,4 +1,4 @@
-# blast-accmap - a tab-separated lists
+# blastaccmap - a tab-separated lists
 #
 # Updated: 2013.1.25
 

diff --git a/docs/format/blast-list.txt → docs/format/blastlist.txt b/docs/format/blast-list.txt → docs/format/blastlist.txt
@@ -1,4 +1,4 @@
-# blast-list - a tab-separated lists
+# blastlist - a tab-separated lists
 #
 # Updated: 2013.1.24