| Previous changeset 14:346ff9ad8c7a (2015-03-20) Next changeset 16:fe4682eb938c (2015-03-23) |
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Commit message:
fix for rankfilter, removed pfd read functional |
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removed:
rankfilter_GCMS/pdfread.py |
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| diff -r 346ff9ad8c7a -r 05ff1c55db84 rankfilter_GCMS/pdfread.py --- a/rankfilter_GCMS/pdfread.py Fri Mar 20 17:10:04 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,214 +0,0 @@\n-"""\n-Copyright (C) 2011 by Velitchka Mihaleva, Wageningen University \n-\n-Permission is hereby granted, free of charge, to any person obtaining a copy\n-of this software and associated documentation files (the "Software"), to deal\n-in the Software without restriction, including without limitation the rights\n-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell\n-copies of the Software, and to permit persons to whom the Software is\n-furnished to do so, subject to the following conditions:\n-\n-The above copyright notice and this permission notice shall be included in\n-all copies or substantial portions of the Software.\n-\n-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\n-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\n-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN\n-THE SOFTWARE.\n-"""\n-\n-import sys\n-import csv\n-\n-def getPDF(filename, print_progress):\n- \'\'\'\n- Parses NIST PDF file\n- @param filename: PDF file to parse\n- \'\'\'\n- NistInput = {}\n- NistInput_missed = {}\n- nist_input = open(filename, \'r\').read()\n-\n- hitid = []\n- rt = []\n- name = []\n- forward = []\n- cas = []\n- reverse = []\n- prob = []\n- lib_id = []\n- nist_id = []\n- missed_compounds = []\n- id_missed_compounds = []\n- formula = []\n-\n- hit_list = nist_input.split(\'** Search Report Page 1 of 1 **\')\n- hit_list.pop(0)\n- #number_hits = range(10)\n- line_id = 0\n- for line in hit_list:\n- line = line.strip().translate(None, \'\\r\')\n- if line != \'\':\n- hits = line.replace(\'\\n\', \' \').replace(\'\\x0c\', \'\').replace(\'^L\', \'\').split(\'Hit\') #solution? : if we wouldn\'t replace the \\n by \' \' but by some special sign, then reading formula would be simpler! \n- #strange....code seems fine actually...debug! See test/data/download.pdf \n- # strange thing is that it looks like the new line does not end up in the text file, eventhough it looks like there is a new line in the pdf...perhaps a bug in the pdf2text command in linux?\n- spec_id = hits.pop(0).split(\' \')[1]\n- j = 0\n- for hh in hits:\n- cell = hh.split(\';\')\n- if print_progress == True:\n- print \'Processing line: \', line_id, \' with length: \', len(cell), \':\\n\\t\', cell\n- line_id += 1\n- if len(cell) == 7: # the compound has CAS number\n- if len(cell[1].split(\':\')) == 2:\n- forward.append((cell[1].split(\':\')[1]).strip())\n- # indication that the name contains the ":". Should join the cells of name_tmp from 1 till end\n- if len(cell[0].split(\':\')) > 2:\n- name_tmp = \':\'.join(cell[0].split(\':\')[1:])\n- else:\n- name_tmp = cell[0].split(\':\')[1]\n- \n- name.append(name_tmp.replace(" ", " ").strip())\n- name_tmp = name_tmp.strip().split(\' \')\n- if name_tmp:\n- # if the name ends with a word that starts with C, F or H, then assume this last word is a formula:\n- if name_tmp[-1][0] == \'C\' or name_tmp[-1][0] == \'F\' or name_tmp[-1][0] == \'H\':\n- formule = (name_tmp[-1])\n- else:\n- formule = (\'not_def\')\n- else:\n- '..b'nd(formule.replace(" ", " "))\n- reverse.append((cell[2].split(\':\')[1]).strip())\n- prob.append(cell[3].split(\' \')[2].replace(\'%\', \'\'))\n- cas.append(\'undef\')\n- lib_id.append((cell[4].split(\':\')[1]).strip())\n- nist_id.append(cell[5].split(\':\')[1].replace(\'.\', \'\').strip())\n- j = j + 1\n-\n- else:\n- missed_compounds.append(hh)\n- id_missed_compounds.append(spec_id)\n-\n- else: # Missing columns, report and quit\n- missed_compounds.append(hh)\n- id_missed_compounds.append(spec_id)\n-\n- for _ in range(j):\n- hitid.append(str(spec_id.replace(" ", " ")))\n- #NB: this is the RT as found in the "id" generated by e.g. msclust, so NOT the RT of the library hit:\n- rt.append(str(float(spec_id.split(\'-\')[3]) / 1e+06))\n-\n- NistInput[\'ID\'] = hitid\n- NistInput[\'R.T.\'] = rt\n- NistInput[\'Name\'] = name\n- NistInput[\'CAS\'] = cas\n- NistInput[\'Formula\'] = formula\n- NistInput[\'Forward\'] = forward\n- NistInput[\'Reverse\'] = reverse\n- NistInput[\'Probability\'] = prob\n- NistInput[\'Library\'] = lib_id\n- NistInput[\'Library ID\'] = nist_id\n- NistInput_missed[\'Missed Compounds\'] = missed_compounds\n- NistInput_missed[\'ID missed Compounds\'] = id_missed_compounds\n-\n- return NistInput, NistInput_missed\n-\n-\n-def convert_pdftotext2tabular(filename, output_file, error_file, print_progress):\n- \'\'\'\n- Converts NIST PDF file to tabular format\n- @param filename: PDF file to parse\n- @param output_file: output file for the hits\n- @param error_file: output file for failed hits\n- \'\'\'\n- [HitList, HitList_missed] = getPDF(filename, print_progress)\n- # save Hitlist as tab seperate file\n- Hitlist_as_text = "\\t".join(HitList.keys()) + "\\n"\n- Hitlist_array_of_array = ([HitList[row] for row in HitList.keys()])\n- Hitlist_as_text += str("\\n".join(["\\t".join(e) for e in zip(*Hitlist_array_of_array)]))\n- output_fh = open(output_file, \'wb\')\n- output_fh.write(Hitlist_as_text)\n- output_fh.close()\n-\n- out_missed_pdf = open(error_file, \'wb\')\n- for x, y in zip(HitList_missed[\'Missed Compounds\'], HitList_missed[\'ID missed Compounds\']):\n- out_missed_pdf.write("Line with incorrect format or unexpected number of fields:\\n")\n- out_missed_pdf.write(\'%s\\n\' % \'\\t\'.join([y, x]))\n- out_missed_pdf.close()\n-\n-\n-def read_tabular(in_csv):\n- \'\'\'\n- Parses a tab-separated file returning a dictionary with named columns\n- @param in_csv: input filename to be parsed\n- \'\'\'\n- data = list(csv.reader(open(in_csv, \'rU\'), delimiter=\'\\t\'))\n- header = data.pop(0)\n- # Create dictionary with column name as key\n- output = {}\n- for index in xrange(len(header)):\n- output[header[index]] = [row[index] for row in data]\n- return output\n-\n-\n-def read_tabular_old(filename):\n- \'\'\'\n- Function to read tabular format (created by convert_pdftotext2tabular)\n- and output a dict with header of columns as key and value is columns of tabular as list\n- @param filename: tabular file to read\n- \'\'\'\n- input_fh = None\n- try:\n- input_fh = open(filename, \'r\')\n- except IOError, error:\n- raise error\n- colnames = input_fh.readline().strip().split(\'\\t\')\n- cells = []\n- for line in input_fh.readlines():\n- cells.append(line.strip().split(\'\\t\'))\n- #transform from row oriented structure to column oriented structure\n- cells = zip(*cells)\n- #store the list of list in form of final output\n- RankFilterGC_format = {}\n- for colnumber in range(len(colnames)):\n- RankFilterGC_format[colnames[colnumber]] = cells[colnumber]\n- return RankFilterGC_format\n-\n-\n-if __name__ == \'__main__\':\n- convert_pdftotext2tabular(sys.argv[1], sys.argv[2], sys.argv[3], True)\n' |