fatool.py added verision 0.0.1 extractNames, cut, extractContigs working

remContigs need testing
	modified:   README.md
	new file:   fatool.py

README.md

@@ -1,3 +1,55 @@
 # FA_TOOL
 
-Command line tool in python. It operates on fa/fasta etc. files.
+Command line tool in python. It operates on fa/fasta etc. files. version: 0.0.1
+
+fatool.py [-h] -f FAFILE  {cut,extractNames,extractContigs,remContigs}
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -f FAFILE, --fafile FAFILE	file to be cut usualy *.fa
+
+fatool commands:
+  {cut,extractNames,extractContigs,remContigs} each has own params, for more details use: command -h
+  
+cut:
+  
+  usage: fatool.py cut [-h] -r RANGE [-o OUTPUT] [-s STEP] [--log LOG]
+
+  optional arguments:
+  -h, --help            show this help message and exit
+  -r RANGE, --range RANGE	cutted sequence length
+  -o OUTPUT, --output OUTPUT	output file default: output.fa
+  -s STEP, --step STEP  step length default: 1
+  --log LOG             log file if not supplied stdout
+  
+extractContigs:
+  
+  usage: fatool.py extractContigs [-h] --list LIST -o OUTPUT [--log LOG] [--multifile]
+
+  optional arguments:
+  -h, --help            show this help message and exit
+  --list LIST           file containing list of contigs one contig per line
+  -o OUTPUT, --output	output file; if --multifile is set output directory
+  --log LOG             log file if not supplied stdout
+  --multifile           if this flag is set each contig will be saved inseparate file
+
+  
+extractNames:
+  
+  usage: fatool.py extractNames [-h] [-o OUTPUT] [--log LOG]
+
+  optional arguments:
+  -h, --help            show this help message and exit
+  -o OUTPUT, --output 	output file if not supplied stdout
+  --log LOG             log file if not supplied stdout
+  
+  remContigs:
+  
+usage: facuter4.py remContigs [-h] --list LIST -o OUTPUT [--log LOG]
+
+  optional arguments:
+  -h, --help            show this help message and exit
+  --list LIST           file containing list of contigs one contig per line
+  -o OUTPUT, --output 	output file if not supplied stdout
+  --log LOG             log file if not supplied stdout
+  

fatool.py

@@ -0,0 +1,202 @@
+# -*- coding: utf-8 -*-
+
+import sys
+import argparse
+import re
+
+
+def main():
+    parser = argparse.ArgumentParser()
+    parser.add_argument('-f', '--fafile', help='file to be cut usualy *.fa', type=argparse.FileType('r'), required=True)
+
+    subparsers = parser.add_subparsers(title='facutter commands', help='each has own params, for more details use: command -h')
+
+    sub_cut = subparsers.add_parser('cut')
+    sub_cut.add_argument('-r', '--range', help='cutted sequence length', type=int, required=True)
+    sub_cut.add_argument('-o', '--output', help='output file default: output.fa', type=argparse.FileType('w'), default='output.fa')
+    sub_cut.add_argument('-s', '--step', help='step length default: 1', type=int, default=1)
+    sub_cut.add_argument('--log', help='log file if not supplied stdout', type=argparse.FileType('w'))
+    sub_cut.set_defaults(func=cut_fa)
+
+    sub_en = subparsers.add_parser('extractNames')
+    sub_en.add_argument('-o', '--output', help='output file if not supplied stdout', type=argparse.FileType('w'))
+    # sub_en.add_argument('--log', help='log file if not supplied stdout', type=argparse.FileType('w'))
+    sub_en.set_defaults(func=extract_names)
+
+    sub_ec = subparsers.add_parser('extractContigs')
+    sub_ec.add_argument('--list', help='file containing list of contigs one contig per line', type=argparse.FileType('r'), required=True)
+    sub_ec.add_argument('-o', '--output', help='output file; if --multifile is set output directory', type=str, required=True)
+    # sub_ec.add_argument('--log', help='log file if not supplied stdout', type=argparse.FileType('w'))
+    sub_ec.add_argument('--multifile', help='if this flag is set each contig will be saved in separate file', action='store_true')
+    sub_ec.set_defaults(func=extract_contigs)
+
+    sub_rc = subparsers.add_parser('remContigs')
+    sub_rc.add_argument('--list', help='file containing list of contigs one contig per line', type=argparse.FileType('r'), required=True)
+    sub_rc.add_argument('-o', '--output', help='output file if not supplied stdout', type=str, required=True)
+    # sub_rc.add_argument('--log', help='log file if not supplied stdout', type=argparse.FileType('w'))
+    sub_rc.set_defaults(func=remove_contigs)
+
+    parser.add_argument('--operator', help='user who have fired script it will be noted in log', type=str)
+    parser.add_argument('--log', help='log file if not supplied stdout', type=argparse.FileType('w'))
+
+    args = parser.parse_args()
+    args.func(args)
+
+
+def make_log(content, lfile):
+    with lfile as f:
+        f.write(content)
+
+
+def cut_fa(args):
+
+    fafile = args.fafile
+    output = args.output
+    split_range = args.range
+    step = args.step
+
+    print 'step used: '+str(step)
+
+    fa = ''  # sequence grabed from file and ceared
+    with fafile as f:
+        # load sequence from file remove first line and all white chars
+        for r in f.readlines()[1:]:
+            fa = fa+r.replace("\r", "").replace("\n", "")
+
+    with output as o:
+        coe = len(fa)  # end of fa position
+        i = 0
+        # N = step*8000
+
+        while i + split_range <= coe:
+            # while curent position + length of frag is less or equal postion of the last char in file.
+            o.write('> frag ' + str(i + 1) + ' : ' + str(i + split_range) + '\n' + str(fa[i:i + split_range]) + '\n')
+            i = i + step
+            # print dot every N split to show that script does not heng.
+            # if(i%N == 0): sys.stdout.write('.')
+
+
+def extract_names(args):
+    fafile = args.fafile
+    output = args.output
+    # sequence title line begining
+    pat = re.compile('^>')
+    if output is None:
+        print 'no output defined results will be print on stdout\n'
+        with fafile as f:
+            for r in f.readlines():
+                if pat.match(r):
+                    print r
+    else:
+        # proceed fafile and save title lines in output file
+        with fafile as f, output as o:
+            for r in f.readlines():
+                if pat.match(r):
+                    o.write(r)
+
+
+def extract_contigs(args):
+    # default all extracted contigs in one file
+    # with flag multifile save each contig to separate file
+    fafile = args.fafile
+    elist = args.list
+    log = args.log
+
+    # counters: extracted contigs and list items
+    excounter = lcounter = 0
+    log_not_found = ''
+
+    print 'extracting contigs'
+    # output to multi files
+    if(args.multifile):
+        output = args.output
+        with elist as cntgs, fafile as f:
+            content = f.read()
+            for r in cntgs:
+                lcounter = lcounter + 1
+                # check if list item is with '>' important to create pattern.
+                if re.match('^>', r.strip()):
+                    pattern = '('+re.escape(r.strip())+'\n[A-Za-z\n]*)>'
+                else:
+                    pattern = '(> '+re.escape(r.strip())+'\n[A-Za-z\n]*|>'+r.strip()+'\n[A-Za-z\n]*)>'
+
+                m = re.search(pattern, content)
+
+                if m:
+                    excounter = excounter + 1
+                    opt = re.sub('[>\*\\\?\<\/]', '', r.strip())
+                    with open(output+'/'+opt+'.fa', 'w') as o:
+                        o.write(m.group(1))
+                else:
+                    # log_content = log_content + 'contig not found: ' + r
+                    log_not_found = 'contig not found: ' + r
+    # output to single file
+    else:
+        output = args.output
+        with elist as cntgs, fafile as f, open(output, 'w') as o:
+            content = f.read()
+            for r in cntgs:
+                lcounter = lcounter + 1
+                # check if list item is with '>' important to create pattern.
+                if re.match('^>', r.strip()):
+                    pattern = '('+re.escape(r.strip())+'\n[A-Za-z\n]*)>'
+                else:
+                    pattern = '(> '+re.escape(r.strip())+'\n[A-Za-z\n]*|>'+r.strip()+'\n[A-Za-z\n]*)>'
+
+                m = re.search(pattern, content)
+
+                if m:
+                    excounter = excounter + 1
+                    o.write(m.group(1))
+                else:
+                    # log_content = log_content + 'contig not found: ' + r
+                    log_not_found = 'contig not found: ' + r
+
+        if(log):
+            log_content = '\nfatools\nlist items:\t'+str(lcounter)+'\nextracted contigs:\t'+str(excounter)+'\n'
+            if log_not_found:
+                log_content = log_content + '\nContigs not found:\n============================================\n'+log_not_found
+            make_log(log_content, log)
+        else:
+            print 'list items: '+str(lcounter)+'; extracted contigs: '+str(excounter)
+            if log_not_found:
+                '\nContigs not found:\n============================================\n'+log_not_found
+
+
+def remove_contigs(args):
+    fafile = args.fafile
+    rlist = args.list
+    output = args.output
+    log = args.log
+    # counters for listitems and removed contigs
+    lcounter = rem_counter = 0
+    with elist as cntgs, fafile as f, open(output, 'w') as o:
+        content = f.read()
+        for r in cntgs:
+            lcounter = lcounter + 1
+            # check if list item is with '>' important to create pattern.
+            if re.match('^>', r.strip()):
+                pattern = '('+re.escape(r.strip())+'\n[A-Za-z\n]*)>'
+            else:
+                pattern = '(> '+re.escape(r.strip())+'\n[A-Za-z\n]*|>'+r.strip()+'\n[A-Za-z\n]*)>'
+
+            if re.match(pattern, content):
+                rem_counter = rem_counter + 1
+            content = re.sub(pattern, '>', content)
+        o.write(content)
+    if(log):
+        make_log('fatool - remContigs:\n list items:\t'+str(lcounter)+'\ncontings rmoved:\t'+str(rem_counter), log)
+    else:
+        print 'list items:\t'+str(lcounter)+'\ncontings rmoved:\t'+str(rem_counter)
+
+
+def split_contigs(args):
+    return 1
+
+
+def statistics(args):
+    return 1
+
+
+if __name__ == '__main__':
+    exit(main())