Changeset 58


Ignore:
Timestamp:
Dec 22, 2009, 8:12:09 AM (15 years ago)
Author:
Rick van der Zwet
Message:

Make the output somehow more clear

File:
1 edited

Legend:

Unmodified
Added
Removed
  • liacs/dbdm/dbdm_4/parse-fasta.py

    r55 r58  
    7373    return(-1,'',head + tail)
    7474
     75# File names
     76file1 = "data/AE005174v2-1.fas"
     77file2 = "data/AE005174v2-2.fas"
    7578
    7679# Get data
    77 file1 = parse_file("data/AE005174v2-1.fas")
    78 file2 = parse_file("data/AE005174v2-2.fas")
     80seq1 = parse_file(file1)
     81seq2 = parse_file(file1)
    7982
    80 file1 = fasta.replace(file1)
    81 file2 = fasta.replace(file2)
     83seq1 = fasta.replace(seq1)
     84seq2 = fasta.replace(seq2)
    8285
    8386# Find overlap
    84 (retval, common, result) = concat(file2,file1)
     87(retval, common, result) = concat(seq2,seq1)
    8588print retval, common
    8689
    87 # Strictly speaking there is a gap of about 4 kbs (4000 bs) between file1 and
    88 # file2, so lets' put that into the the statistics as well. Due to circular
     90print file1
     91stats(seq1)
     92print file1
     93stats(seq1)
     94
     95# Strictly speaking there is a gap of about 4 kbs (4000 bs) between seq1 and
     96# seq2, so lets' put that into the the statistics as well. Due to circular
    8997# nature, does not matter wether we add it in the beginning or in the end
     98print "Total (inc 4 kbs gap (n))"
    9099result = result + "n" * 4000;
    91100stats(result)
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