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1 #!/usr/bin/env python
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2 """
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3 Input: fasta, minimal length, maximal length
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4 Output: fasta
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5 Return sequences whose lengths are within the range.
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6 """
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7 import sys, os
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8
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9 assert sys.version_info[:2] >= ( 2, 4 )
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10
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11 def stop_err( msg ):
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12 sys.stderr.write( msg )
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13 sys.exit()
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14
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15 def __main__():
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16 infile = sys.argv[1]
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17 title_col = sys.argv[2]
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18 seq_col = sys.argv[3]
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19 outfile = sys.argv[4]
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20
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21 if title_col == None or title_col == 'None' or seq_col == None or seq_col == 'None':
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22 stop_err( "Columns not specified." )
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23 try:
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24 seq_col = int( seq_col ) - 1
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25 except:
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26 stop_err( "Invalid Sequence Column: %s." %str( seq_col ) )
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27
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28 title_col_list = title_col.split( ',' )
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29 out = open( outfile, 'w' )
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30 skipped_lines = 0
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31 first_invalid_line = 0
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32 invalid_line = ""
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33 i = 0
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34
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35 for i, line in enumerate( open( infile ) ):
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36 error = False
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37 line = line.rstrip( '\r\n' )
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38 if line and not line.startswith( '#' ):
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39 fields = line.split( '\t' )
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40 fasta_title = []
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41 for j in title_col_list:
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42 try:
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43 j = int( j ) - 1
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44 fasta_title.append( fields[j] )
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45 except:
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46 skipped_lines += 1
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47 if not invalid_line:
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48 first_invalid_line = i + 1
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49 invalid_line = line
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50 error = True
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51 break
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52 if not error:
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53 try:
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54 fasta_seq = fields[seq_col]
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55 if fasta_title[0].startswith( ">" ):
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56 fasta_title[0] = fasta_title[0][1:]
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57 print >> out, ">%s\n%s" % ( "_".join( fasta_title ), fasta_seq )
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58 except:
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59 skipped_lines += 1
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60 if not invalid_line:
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61 first_invalid_line = i + 1
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62 invalid_line = line
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63 out.close()
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64
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65 if skipped_lines > 0:
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66 print 'Data issue: skipped %d blank or invalid lines starting at #%d: "%s"' % ( skipped_lines, first_invalid_line, invalid_line )
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67
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68 if __name__ == "__main__" : __main__() |
